Class II Lysyl-tRNA Synthetase

The Class II lysyl-tRNA synthetase (LysRS-II) is an enzyme that plays a crucial role in protein synthesis by catalysing the attachment of the amino acid lysine to its cognate tRNA: $ \text{Lys} + \text{tRNA}^\text{Lys} + \text{ATP} \xrightarrow{\text{LysRS-II}} \text{Lys-tRNA}^\text{Lys} + \text{AMP} + \text{PP}_i $ The three-dimensional structure of LysRS-II closely resembles that of [AspRS](/class2/asp1/), [AsnRS](/class2/asn/), and [AsxRS](/class2/asp2/), with an N-terminal [anticodon binding domain](/superfamily/class2/Anticodon_binding_domain_DNK/) and a C-terminal catalytic domain. The four members have quite similar catalytic domains and constitute subclass IIb (Cusack et al., 1991; Valencia-Sánchez et al., 2016). The subclass IIb synthetases of many eukaryotes contain a flexible domain at their N-termini, which helps to anchor the synthetase onto the tRNA (Frugier et al., 2000). The N-terminal anticodon binding domain binds the second and third positions of the anticodon (Cusack et al. 1996). This enables binding specificity towards $\text{tRNA}^\text{Lys}$, as opposed to$\text{tRNA}^\text{Asn}$, as their anticodon binding domains are similar, and their first two codon positions are identical in most genetic codes (AAA and AAG for Lys; AAC and AAT for Asn). The C-terminal catalytic domain of LysRS-II is quite typical for a Class II AARS. Like most members of the superfamily, ATP binding is coordinated by the arginine tweezers, located in motifs 2 and 3 (Kaiser et al., 2018). The catalytic domain of AsnRS, much like the other members of subclass IIb, is characterised by the subclass IIb insertion modules 1 and 2 (Douglas et al. 2023). In the active site, three metal ions bind to the $\beta$ and $\gamma$ phosphates of ATP (Blanquet et al. 2005). LysRS-II displays negative cooperativity between its subunits, meaning that substrate binding in the active site of one subunit lowers the catalytic activity of the other (Hughes et al. 2003). Editing in LysRS-II occurs at the pre-transfer level, without the need for a dedicated editing domain. This process has been characterised for methionine, leucine, cysteine, alanine, threonine, homocysteine, homoserine, and ornithine (Jakubowski 1997, 1999). Most archaea, and some bacteria, instead have a Class I [LysRS-I](/class1/lys). These two variants have distinct evolutionary origins and are often presented as an example of convergent evolution. Some bacterial species, including *Escherichia coli* have two copies of the class II LysRS gene, with around 90% sequence identity (Blanquet et al. 2005).

References

Cusack, S., A. Yaremchuk, and M. Tukalo. "The crystal structures of T. thermophilus lysyl‐tRNA synthetase complexed with E. coli tRNA (Lys) and a T. thermophilus tRNA (Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl‐adenylate analogue." The EMBO journal 15.22 (1996): 6321-6334. Douglas, J, Bouckaert, R., Carter, C., & Wills, P. R. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Research Square (2023). Cusack, Stephen, Michael Härtlein, and Reuben Leberman. "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases." Nucleic acids research 19.13 (1991): 3489-3498. Valencia-Sánchez, Marco Igor, et al. "Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases." Journal of Biological Chemistry 291.28 (2016): 14430-14446. Blanquet, Sylvain, et al. "The Aminoacyl-tRNA Synthetases" CRC Press (2005): Chapter 20: Class II Lysyl-tRNA Synthetases. Gomez, Miguel Angel Rubio, and Michael Ibba. "Aminoacyl-tRNA synthetases." Rna 26.8 (2020): 910-936. Kaiser, Florian, et al. "Backbone brackets and arginine tweezers delineate class I and class II aminoacyl tRNA synthetases." PLoS computational biology 14.4 (2018): e1006101. Jakubowski, Hieronim. "Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases." Biochemistry 36.37 (1997): 11077-11085. Jakubowski, Hieronim. "Misacylation of tRNALys with noncognate amino acids by lysyl-tRNA synthetase." Biochemistry 38.25 (1999): 8088-8093. Hughes, Samantha J., et al. "Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment." BMC Structural Biology 3.1 (2003): 1-20. Frugier, Magali, Luc Moulinier, and Richard Giegé. "A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding." The EMBO Journal 19.10 (2000): 2371-2380.